[BioC] getSequence from biomaRt changes the order of sequences given as input - is it normal?

Emmanuel Levy emmanuel.levy at gmail.com
Mon Jan 7 19:40:22 CET 2013


Hello,

I started using biomaRt and find it really convenient. One thing I
noticed is that the function getSequence reorders the sequences when
multiple ids are given as input.

I'm not sure if this is normal or if I missed an option?

Here is what I do:

> ensembl.yeast = useMart(biomart="ensembl", dataset = "scerevisiae_gene_ensembl")
> ids = c("S000005528","S000000221" ,"S000005993", "S000003105", "S000004200")
> yeast.gen = getSequence( id=ids, mart=ensembl.yeast, seqType=c("cdna"), type="sgd_transcript" )
> yeast.gen[[2]]
[1] "S000005528" "S000004200" "S000003105" "S000000221" "S000005993"

So the ID No. 5 is now No. 2. It would be convenient if the sequences
retrieved would be in the order specified by "id". Not that it's a big
problem but just a thought ... or maybe I missed something?

All the best,

Emmanuel



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